Affymetrix microarrays use this base pairing attraction — a property known as hybridization — to help researchers identify each SNP genotype. The sequencing work of the Human Genome Project told us the DNA sequence around any SNP we'd like to genotype. Microarrays use that information to determine SNP genotype. Because C always pairs with G, and T always pairs with A, if you know that one side of the chain is ATTCATG (the SNP is in the middle), you don't even need to see the other side — you know it's TAAGTAC. The SNP genotype would be C/G. Likewise, if you know that sequence of one strand is ATTTATG, you automatically know the sequence of the other side is TAAATAC. And this DNA would have a T/A SNP genotype.

So, if you're not sure what the SNP genotype is, all you have to do is look at both strands. If a person's DNA matches ATTCATG then you know they are a C/G genotype. If a person's DNA matches the ATTTATG strand then you know they are the T/A genotype.

But what's amazing about Affymetrix DNA analysis SNP arrays is that they don't just do it one SNP at a time. The arrays tell you whether a person has a single SNP, they tell you whether they have 100,000 SNPs or more. To understand how, let's look at how an actual Affymetrix DNA analysis array works.